The Philippines Navy says it has detained 35 suspected Filipino militants as they sought to sail home from a military offensive against them in the Malaysian state of Sabah.

Regional military chief Rey Ardo said the militants are believed to be remnants of a band of up to 300 followers of a self-proclaimed Filipino sultan who entered Sabah a month ago to stake a territorial claim to the area.

"They were coming back (home)... they are armed," Lieutenant-General Ardo said.

Navy spokesman Lieutenant-Colonel Gregory Fabic said the 35 people seized were on two small boats intercepted by two navy patrol vessels on the Philippine side of the sea border with Malaysia.

Lieutenant-General Ardo said the militants were sailing to a Philippine island about 60 kilometres from the area of Sabah at the heart of the security offensive.

The self-proclaimed Sultan of Sulu Jamalul Kiram III, whose ancestors ruled over parts of the what is now the southern Philippines and Sabah centuries ago, vowed his men would not leave until Malaysia recognised their territorial claims.

However, after a stand-off that lasted more than two weeks, Malaysian security forces launched a major operation against the gunmen.

Malaysian authorities have reported that 64 people have been killed, mostly militants, and 97 followers of the sultan have been arrested in Sabah.

Security operations are continuing.

Sabah protest

Philippine civilian groups will demonstrate outside the Malaysian embassy in Manila on Thursday, to protest against what they say is an assault on Filipinos by Malaysian security forces.

Protest organiser, the Party of the Labouring Masses, says some Filipino settlers have since fled Sabah, with 500 seeking refuge in Philippine Tawi Tawi.

Party of the Labouring Masses' Chairman, Sonny Melencio, told Radio Australia's Asia Pacific that it was in the interest of both the Philippines and Malaysia that correct information is published "on what's happening there".

"What the (Philippine) papers are saying, that there is a news blackout in the area and the Filipino media are not allowed to cover what's happening there in the area," he said.